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<p><center><h1>An Open Access Knowledge Database Devoted to Viruses<br>
and Mobile Genetic Elements</h1></center></p>

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Intro

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Wikiadmin: /* Mobile Genetic Elements */

== GyDB project ==

The GyDB project pursues the fascinating goal of analyzing and classifying the non-redundant diversity of mobile genetic elements in the context of the tree of life and based on their evolutionary profiles. The emergence and subsequent role played by viruses and mobile genetic elements in the history of life is an unclear yet exciting object of investigation, where researchers try to discern relevant aspects of the molecular changes responsible for various characteristics in the biological organisms related with horizontal transfer, infection and disease.

The most captivating aspect of our project is that we dedicate a share of our efforts to the interpretation of our analyses, we pay special attention to non-redundant elements displaying a certain degree of distance and how they can be collectively aligned or related, in terms of protein domain architecture with other lineages and elements. This is an effort worth making, as we are able to infer the evolutionary perspectives of the elements we classify based on the common internal region. The GyDB project is thus a highly informative database established within an evolutionary context of classification. We think this strategy will allow the GyDB to enable exciting insights leading to a better understanding of the taxonomy and evolutionary history of the elements we classify. Hence, although you may detect imperfections and lacks (new evidence concerning mobile genetic elements is continuous), this is however, what makes this project exciting; one research delivers one conclusion that drives you to another goal, the principal aim which with we have built this database.

Due to their impressive molecular diversity, the GyDB is a long-term project that has been arranged in a database in continuous progress that must be achieved in stages. Taking this into primary consideration this second release (GyDB 2.0) has been powered by a wiki content management system to let other researchers participate in the project. The current database scope is LTR retroelements and their relatives. On the basis of this scope, the first release focused on the evolutionary relationships of ''Ty3/Gypsy'' and ''Retroviridae'' LTR retroelements, and clan AA of Aspartic Peptidases. GyDB 2.0 is an update based on the analysis of ''Ty3/Gypsy, Retroviridae, Ty1/Copia'' and ''Bel/Pao'' LTR retroelements and the ''Caulimoviridae'' pararetroviruses of plants.

== Mobile Genetic Elements ==

In a broad sense, Mobile Genetic Elements (MGEs) can be considered as segments of DNA somehow involved in the movement of DNA within genomes (intracellular mobility) and between cells (intercellular mobility) ([[literature:100836|Frost ''et al''. 2005]]). Such definition would include genomic islands, bacteriophages and plasmids along with transposable elements (TEs). The latter are initially the elements we are going to focus on at GyDB considering MGEs as self-contained genomic units capable of proliferating within their host genomes.

Since the existence of mobile DNA was first suggested by McClintock ([[Literature:48820|McClintock 1948]]) MGEs have been important object of study in multiple areas of research ([[Literature:36623|Kazazian 2004]]). Nearly all fit into two major categories of TEs classified by their mechanisms:

*'''Class I''' are retroelements ([[Literature:76300|Temin 1989]]) that mediate their transposition life cycle through an RNA-DNA reverse transcription process. In collective, all reverse transcriptase (RT) dependent retrotransposons and retroviruses (detailed description concerning this group will be found at [[Retroelements|Retroelements]]) .
<center>[[file:MGE1.png]]</center>
<br />
<center>[[file:MGE3.png]]</center>
<center>Class I schematic mechanism of transposition and genomic structure of main groups</center>

*'''Class II''' are DNA-based transposons that move directly from one position to another in host genomes ([[Literature:48820|McClintock 1948]]; [[Literature:85374|Mizuuchi 1992]]; [[Literature:15303|Craig ''et al''. 2002]]).
<center>[[file:MGE2.png]]</center>
<br />
<center>[[file:MGE4.png]]</center>
<center>Class II schematic mechanism of transposition and genomic structure of main groups</center>

Transposable Elements are ubiquitous in nature, quite abundant and irregularly distributed within genomes. They can act as mutagenic agents, generate DNA rearrangements, influence gene expression and, in short, play an important role in the evolution of the host genome. Identification, characterization and analysis of TEs and their dynamics are important for a better understanding of the structure and evolution of both, genomes and mobile DNA themselves ([[literature:100837|Holmes 2002]]; [[literature:100838|Kidwell & Lisch 1997]]). However, scientific interest on TEs lies not only in derivative evolutive studies (as they are considered fossil markers), but also in its role in host genomes, its usefulness as biotechnological tools even for genetic medical applications and other potential future implications ([[literature:100839|Levin & Moran 2011]]; [[literature:100833|Nesmelova & Hackett 2010]]; [[literature:30832|Hickman ''et al''. 2005]]).

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<p><center><h1>An Open Access Knowledge Database Devoted to Viruses<br>
and Mobile Genetic Elements</h1></center></p>

<p>[[File:New_logo_new.jpg|center]]</p>

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2020-12-30T12:07:58Z

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<h1 style="color:red">This site is currently under maintenance. We are upgrading the wiki to a new version.</h1>

<p><center><h1>An Open Access Knowledge Database Devoted to Viruses<br>
and Mobile Genetic Elements</h1></center></p>

<p>[[File:New_logo_new.jpg|center]]</p>

Main Page

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<h1 style="color:red">This site is currently under maintenance</h1>

<p><center><h1>An Open Access Knowledge Database Devoted to Viruses<br>
and Mobile Genetic Elements</h1></center></p>

<p>[[File:New_logo_new.jpg|center]]</p>

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Mobilomics

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Mobilomics

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Wikiadmin: Página creada con «The Server "Mobilomics" is an in-progress repository of databases with MGE features annotated from distinct organisms. In that sense, each organism mobilome can be consider…»

The Server "Mobilomics" is an in-progress repository of databases with MGE features annotated from distinct organisms. In that sense, each organism mobilome can be considered as an ongoing project and, following the general collaborative aim of GyDB, we kindly encourage other researchers interested in the topic of mobile DNA elements "within-organisms" to contribute with data from any species or diverse improvement suggestions.

As an initial approach we have deposited the annotations of the complete set of LTR retroelements (LTR retrotransposons and retroviruses) identified in the first draft genome assembly of the pea aphid Acyrthosiphon pisum which is available within the NCBI ftp site or alternativelly through the Baylor College of Medicine Human Genome Sequencing Center ftp site.

You can access to detailed annotation data for each organism in the list below by clicking its name. You can also compare your query sequence to the database of your interest (<img src="/gydbModules/mobilomics/images/mobilomics_blast.jpg" /> icon) and download the whole annotation mobilomic database of an organism (<img src="/gydbModules/mobilomics/images/mobilomics_download.jpg" /> icon).

Literature search

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Phylogeny:GagPol

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{{Phylogeny
|map=<imagemap>
Image:GagPol.png|center
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rect 340 1024 368 1038 [[Element:CAEV|CAEV]]
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rect 340 732 367 746 [[Element:Mdg3|Mdg3]]
rect 340 741 384 755 [[Element:Blastopia|Blastopia]]
rect 340 723 382 737 [[Element:Micropia|Micropia]]
rect 340 596 364 610 [[Element:Woot|Woot]]
rect 340 605 378 619 [[Element:Osvaldo|Osvaldo]]
rect 340 614 365 628 [[Element:Circe|Circe]]
rect 340 623 373 637 [[Element:Ulysses|Ulysses]]
rect 340 641 362 655 [[Element:Cer3|Cer3]]
rect 340 650 362 664 [[Element:Cer2|Cer2]]
rect 340 632 362 646 [[Element:Cer1|Cer1]]
rect 340 705 362 719 [[Element:Cer5|Cer5]]
rect 340 714 362 728 [[Element:Cer6|Cer6]]
rect 340 696 362 710 [[Element:Cer4|Cer4]]
rect 340 687 377 701 [[Element:Gulliver|Gulliver]]
rect 340 678 361 692 [[Element:Mag|Mag]]
rect 340 668 367 682 [[Element:SURL|SURL]]
rect 340 659 368 673 [[Element:Cigr-1|Cigr-1]]
rect 340 31 365 45 [[Element:Cgret|Cgret]]
rect 340 40 364 54 [[Element:Pyret|Pyret]]
rect 340 22 371 36 [[Element:Skippy|Skippy]]
rect 340 13 362 27 [[Element:Cft-1|Cft-1]]
rect 340 49 371 63 [[Element:marY1|marY1]]
rect 340 59 387 73 [[Element:Sushi-ichi|Sushi-ichi]]
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rect 340 77 374 91 [[Element:Dane-1|Dane-1]]
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rect 340 231 356 245 [[Element:Del|Del]]
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rect 340 259 373 273 [[Element:Bagy-1|Bagy-1]]
rect 340 241 382 255 [[Element:Peabody|Peabody]]
rect 340 277 367 291 [[Element:Ty3-1|Ty3-1]]
rect 340 286 375 300 [[Element:Skipper|Skipper]]
rect 340 268 363 282 [[Element:Tse3|Tse3]]
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rect 340 313 372 327 [[Element:Kabuki|Kabuki]]
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rect 340 541 359 555 [[Element:Tft2|Tft2]]
rect 340 477 363 491 [[Element:Ogre|Ogre]]
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rect 340 750 369 764 [[Element:WdSV|WdSV]]
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</imagemap>
|method=Phylogenetic reconstruction inferred based on the concatenated protein product
encoded by the gag-pro-pol internal region common to Ty3/Gypsy and Retroviridae LTR
retroelements using FelsensteinÂ´s protein sequence parsimony method based on (Eck
and Dayhoff 1966) and (Fitch 1971) to generate a majority-rule consensus tree
(Margush and McMorris 1981). As majority-rule consensus tree usually consists of all
groups that occur more than 50% of the time, we take consensus values upper to 50 as
an equivalent-bootstrapping reference.
|citation=citation_test
}}

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Elements

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[classified_elements]

Elements

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TestPage

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[classified_elements]

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LTR Retroelements

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Wikiadmin: Página creada con «== '''Introduction''' == Retroelements with long terminal repeats (LTRs) represent one of the four major groups of retrotranscribing mobile genetic elements. This system i…»

== '''Introduction''' ==
Retroelements with long terminal repeats (LTRs) represent one of the four major groups of retrotranscribing mobile genetic elements. This system includes the broad range of LTR retrotransposons and retroviruses present in animals, plants and fungi (for more information in this topic, see[[Retroelements| Retroelements]]), and other non-autonomous retroelements evolved from LTR retroelements. We additionally consider caulimoviruses of plants within the system of autonomous LTR retroelements because of their common evolutionary relationship with them based on the gag-pol region.

== '''Autonomous LTR retroelements''' ==
These are composed of an internal coding region bounded by LTRs of variable size. The LTRs usually end in short inverted repeats, they do not encode for any known protein but contain promoters and features associated with the element transcription ([[Literature:40507|Kumar and Bennetzen 1999]]). LTR retroelements have a Primer Binding Site (PBS) as well as a Polypurine Tract (PPT) downstream to the 5´LTR and upstream to the 3´LTR, respectively (for more information, see[[LTRs| LTRs]]). The internal region contains the characteristics gag and pol (and env in the case of retroviruses) ORFs, which encode for the different protein products required for the replication cycle and transposition of LTR retroelements ([[Literature:88885|Eickbush and Jamburuthugoda 2008]]). The replication cycle of LTR retrotransposons includes both nuclear and cytoplasmic stages. Inserted LTR retroelements are transcribed into mRNAs which are then exported to the cytoplasm to form virus-like particles (VLPs) and retrotranscribed cDNA copies that go back to the nucleus for integration in the host's DNA genome. Based on sequence similarity and other features LTR retroelements can be classified into four major families called ''Ty1/Copia'', ''Ty3/Gypsy'', ''Bel/Pao'' and ''Retroviridae''.
=== ''Ty1/Copia'' ===
''Ty1/Copia'' elements are abundant in species ranging from single-cell algae to superior plants and animals. The Ty1/Copia internal region encodes for the typical gag and pol polyproteins but differ from other LTR retrotransposons in the ORF position of integrase (INT), which maps after to protease (PR). The classification of this family is in continous progress. According to the ICTV, the ''Ty1/Copia'' family (taxonomically the ''Pseudoviridae'') was originally divided into three genera: Pseudovirus, Hemivirus and Sirevirus (for more details, see [[Literature:100591| Boeke ''et al''. 2005]]). However, a recent study ([[Literature:100596|Llorens ''et al''. 2009]]) shows that the diversity of ''Ty1/Copia'' LTR retroelements is greater than this original classification. On the other hand, genomic studies have revealed the presence of an ''env''-like ORF in some ''Ty1/Copia'' species belonging to the genus Sirevirus ([[Literature:41869|Laten ''et al''. 1998]]; [[Literature:29886|Havecker ''et al''. 2005]]). Also, some ''Ty1/Copia'' elements (called ''CoDi-A'') described in diatoms encode for integrases (INTs) carrying a putative chromodomain similar to that found in the INTs coded by ''Ty3/Gypsy'' chromoviruses (for more information about this family, see [[Ty1/Copia| ''Ty1/Copia'']] family).

=== ''Ty3/Gypsy'' ===
''Ty3/Gypsy'' LTR retroelements also spread in animal, plant and fungal organisms. In almost (but not all) ''Ty3/Gypsy'' LTR retroelements ''int'' maps after to the Ribonuclease H (RH) in the pol polyprotein ([[Literature:88885|Eickbush and Jamburuthugoda 2008]]). The exception is the ''Ty3/Gypsy'' lineage called ''Gmr1'' ([[Literature:26669|Goodwin and Poulter 2002]]) which show an ORF organization identical to that of ''Ty1/Copia'' elements. The classification of ''Ty3/Gypsy'' LTR retroelements is also an in-progress matter. ICTV originally classified this family into two major genera, namely Metavirus and Errantivirus, based on the presence or absence of a third ORF ''env'' (''Metaviridae'' group, [[Literature:100590|Eickbush ''et al''. 2005]]). However, increasing evidences have revealed that these two genera include retroviruses and retrotransposons (for more details, see [[Ty3/Gypsy|''Ty3/Gypsy'']] family).

=== ''Bel/Pao'' ===
''Bel/Pao'' LTR retroelements have been only described in metazoan genomes. This family includes both LTR retrotransposons and retroviruses, as it is now known that some ''Bel/Pao'' species encode for putative ''env''-like genes ([[Literature:8238|Bowen and McDonald 1999]]; [[Literature:29887|Havecker ''et al''. 2004]]; [[Literature:88885|Eickbush and Jamburuthugoda 2008]]). These LTR retroelements show the same genomic ORF organization than ''Ty3/Gypsy'' family and are taxonomically known as semotiviruses (according to the ICTV, [[Literature:100590|Eickbush ''et al''. 2005]]). For more information, see[[Bel/Pao| ''Bel/Pao'']] family.

=== ''Retroviridae'' ===
''Retroviridae'' constitute a family of retroviruses which specifically inhabit or circulate in the genomes of vertebrates. The gag-pol-env genome ORF organization of the ''Retroviridae'' is similar to that of ''Ty3/Gypsy'' and ''Bel/Pao'' simple retroviruses. In most cases the multiple distinct ''Retroviridae'' species are complex retroviruses that incorporate in their genomes some additional accessory genes which are necessary for the replication cycle and transmission from a host into another. According to the ICTV ([[Literature:100589|Fauquet ''et al''. 2005]]), the ''Retroviridae'' can be divided into seven genera namely ''Alpha-'', ''Beta-'', ''Gamma-'', ''Delta-'', ''Epsilon-'', ''Spumaretroviridae'' and ''Lentiviridae'' (for further information, see [[Retroviridae |''Retroviridae'']] family).

<center>[[File:auton_LTRs.jpg]]</center>

===Caulimoviruses===
Plant caulimoviruses (''Caulimoviridae'') are double-stranded DNA unenveloped pararetroviruses that do not regularly integrate into the host genome for replication. Caulimoviral particles could be either bacilliform or isometric. According to ICTV, this family comprises six genera: ''Caulimovirus'', ''Soymovirus'', ''Cavemovirus'', ''Tungrovirus'', ''Badnavirus'' and ''Petuvirus'' ([[Literature:100592|Hull ''et al''. 2005]]). These replicate in plants via a RNA intermediate evolved from LTR retroelements ([[Literature:86892|Bousalem ''et al''. 2008]]). Despite caulimoviruses are not LTR retroelements and have not LTRs, they show a gag-PR-RT-RH genomic architecture similar to that of LTR retroelements. Additionally, caulimoviruses encode for other proteins required in their replication cycle and transmission (see the figure below, which represents the genome structure of the ''Cauliflower mosaic virus'' (CaMV) ([[Literature:100593|Franck ''et al'' 1980]]; [[Literature:100594|Stavolone ''et al''. 2005]])).
That is, the distinct caulimoviruses species show particular ORFs encoding for both structural and non structural proteins - movement protein, proteases, reverse transcriptase, RNase H and transactivator protein - as well as some proteins which function is unknown yet.
<center>[[File:Caulimovirus.jpg]]</center>

== '''Non-autonomous LTR retroelements''' ==
This is a family of retrotransposons showing LTRs, PBS and PPT sequences characteristics of autonomous LTR retrotransposons but usually lacking of coding capacity. Two classes of non-autonomous LTR retrotransposons have been described: the LArge Retrotransposons Derivatives ('''LARDs''') and the Terminal-repeat Retrotransposons In Miniature ('''TRIMs'''). These elements probably need the help of mobility-related proteins encoded by other functional (autonomous) retrotransposons. To date, non-autonomous LTR retroelements have been only described in plants. As there is no intermediate sequences described between TRIMs and LARDs, these appear to follow different replicational or life-cycle strategies and probably have distinct histories ([[Literature:35840|Kalendar ''et al''. 2004]]).

==='''LARDs'''===
LARDs range from 5.5 kb to 8.5 kb and have large-conserved-no coding internal domains of 3.5 kb flanked by long LTRs (4.5 kb). Although LARD elements have been found throughout the ''Triticeae'' tribe (they have been primarily described from barley and related grasses and called ''Sukkula''-like elements) they have also been detected in grass species outside the ''Triticeae'' and in rice ([[Literature:100595|Jiang ''et al''. 2002a]]; [[Literature:34872|2002b]]). It has been suggested that LARDs evolve from ''Ty3/Gypsy'' LTR retroelements as they apparently use (for replication and integration) distinct protein products encoded by their putative ''Ty3/Gypsy'' LTR retroelements partners ([[Literature:35840|Kalendar ''et al''. 2004]]).
==='''TRIMs'''===
TRIMs elements are less than 540 bp in size. They show a small non-coding central domain of 100–300 bp which contains PBS and PPT motifs and that is flanked by small LTRs of 100–250 bp in size. The complete lack of coding capacity makes it impossible to classify TRIMs elements conventionally into ''Ty1/Copia'' or ''Ty3/Gypsy'' families ([[Literature:83212|Witte ''et al''. 2001]]). These elements have been described in both monocotyledonous and dicotyledonous plant species and seem to be involved actively in the restructuring of plant genomes ([[Literature:83212|Witte ''et al''. 2001]]).

<center>[[File:non-auton_LTRs.jpg]]</center>

[[Category:Retroelements]]